Genomic Profiling
(Lisa White, Ph.D., Director;
Eastwood Leung , Ph.D., Co-Director)
The Dan L. Duncan Cancer Center Genomic Profiling Shared Resource combines the resources of the BCM Microarray Core Facility and the Texas Children’s Hospital.
- Our goal is to provide investigators access to state-of-the-art quality microarray technology and services for both transcriptional and genomic profiling.
- Our purpose is to assist researchers in utilizing microarray technology (either spotted glass or commercial), employing good experimental design, and providing data management and data analysis resources.
Services at Baylor College of Medicine
Services at Texas Children’s Hospital
Services at Baylor College of Medicine
Experimental Design Consultation
All users of the DLDCC GPSR are required to meet with either the director or co-director to discuss their proposed research. These meeting are generally for one hour and include explanations of the different array technology options available to the user and strategies on how the different array applications will benefit the user’s research. At this time, pricing is also discussed with the user and experiments are designed that maximizes the numbers of samples to achieve the most power while keeping the experiment affordable to each user.
Clone Repository Services
The GPSR owns thousands of cDNA clones and these are provided by request to investigators. Users can search our Mouse and Human clone sets for genes they are interested in for use in verifying results from gene expression or other experiments. Clone sets are listed below and can be searched through the Core website. Mouse NIA 15K, Mouse BMAP 32K, Mouse BMAP Retina, Mouse NIA 7.4K, Mouse 3.5K Pancreas, Mouse RIKEN FANTOM1 21K, Human HTVV 40K (sequence verified). The GPSR has implemented a web-based clone search since the P30 submission that makes identifying the cDNA clone of interest easy and efficient.
Sample Quality Assurance/Quality Control
Sample quality is one of the most important factors for producing good data. All users intending to utilize one of the genomic profiling services offered in the GPSR must submit the samples to the facility prior to requesting other services. This service is also open to users who just want to gauge the quality of their sample without using our other services. Samples are submitted to the facility through our web-based LIMS and tested for integrity, concentration, and purity. RNA and cDNA samples are analyzed on the Agilent 2100 Bioanalyzer (Agilent Technologies) that utilizes Lab-on-a-Chip technology (Caliper Life Sciences) and the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). Genomic DNA samples are tested using the NanoDrop ND-1000 spectrophotometer and integrity is assessed using agarose gel electrophoresis.
Gene Expression Profiling
Affymetrix gene expression profiling
This GeneChip platform is a commercially available DNA-based silicon wafer populated with oligonucleotides that represent the genes and expressed sequence tags (EST) currently known for a particular genome. Arrays are available in a variety of species, although the most frequently used in our facility are mouse, human, and rat. Gene expression applications are: whole genome transcriptome analysis, alternative splicing analysis, and whole genome tiling. There are two labeling technologies for these applications, the Eberwine 3’ IVT and a whole transcriptome labeling coupled with ribosome reduction.
Spotted glass array-based expression profiling
We offer several spotted glass array platforms for gene expression profiling including Agilent, and Nimblegen. Samples can be analyzed with one or two color labeling. Again, multiple species-specific arrays are available for use to our users with the majority use being human and mouse. Nimblegen arrays are used almost exclusively for prokaryotic profiling. In addition to classical profiling, we also offer microRNA profiling using Agilent or Exiqon arrays.
Luminex bead-based expression profiling
Multiplex expression analysis utilizing Luminex beads is available through the GPSR. This technology allows us to offer customized bead panels to measure expression of mRNA (Panomics) and microRNAs (FlexmiR). This is a robust platform that will enable researchers to measure expression of a select number of genes at a reasonable price.
NanoString nCounter Digital Gene Expression platform
The nCounter Analysis System uses a novel digital technology that is based on direct multiplexed measurement of gene expression and offers high levels of sensitivity (500 attomolar <1 copy per cell) and precision. The technology uses molecular barcodes and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction.
SuperArray QPCR Gene Expression platform
The GSPR is now offering SuperArray Bioscience services. These 96-well QPCR arrays provide researchers access to new tools for profiling gene expression focused on a biological pathway or disease state. The RT2 Profiler PCR Array System allows researchers to easily determine changes in gene expression for up to 96 genes of interest. Over 100 PCR Arrays are available covering Cytokines, Apoptosis, Cancer, Signal Transduction, and many other topics. They are also easily customized to fit any list of genes.
Genomic DNA-Based Profiling
SNP Genotyping Platform
DLDCC members can utlize the Affymetrix SNP 6.0 Genechip (1.8 million probe array) through the GPSR. SNP Genotyping can be used for gene association studies as well as studies assaying copy number changes in samples (or array CGH).
Array Comparative Genomic Hybridization (aCGH)
Genomic copy number changes can be assayed using several platforms in the GPSR including Agilent, Nimblegen, and Affymetrix SNP 6.0. Chromosomes are known to have numerous different copy number aberrations in cancerous cells and many researchers are now utilizing this service.
DNA-based arrays (not aCGH)
The GPSR also offers ChIP-chip analysis for protein-DNA interactions as well as assaying epigenetic changes such as methylation and chromatin modeling. Platforms available to assay ChIP-chip and methylation, etc. are Affymetrix (whole genome tiling, promoter), Agilent (promoter, custom tiling), and Nimblegen (whole genome tiling, custom tiling).
Data Analysis
The GPSR works in conjunction with the DLDCC Biostatistics Shared Resource. Users who intend to request data analysis (for SNP genotyping and mRNA expression) help are directed to the Biostatistics Resource for discussions that includes experimental design/consultation. Other analyses are available through the GPSR and they include aCGH analysis, miRNA expression analysis, and Illumina bead-array analysis. The GPSR also collaborates closely the with Bioinformatics Research Center here at BCM for aid in pathway analysis and other database-related issues.
Contact Information
Lisa D. White, Ph.D.
Director, Genomic Profiling Shared Resource, Dan L. Duncan
Cancer Center
Asst. Professor, Dept. Molecular & Human Genetics
Director, Microarray Core Facility
Technical Director, Chromosomal Microarray Analysis,
Molecular Genetics Laboratories
Baylor College of Medicine
One Baylor Plaza, Rm. 333E, Mailstop: BCM225
Houston, TX 77030
Tel: 713-798-7607 Fax: 713-798-7610
Email: lisaw@bcm.edu
http://www.bcm.edu/microarray
Staff
Director: Lisa D. White, Ph.D. Administrative Contact: Maria Rodriguez Laboratory Manager: Laura Liles Garza Research Assistant: Hillary Lewis Research Technician: Nalaka Senaratne Research Technician: Nick Leclair Research Technician: Mylinh HoangLocation
Baylor College of Medicine
One Baylor Plaza, Room 325E
Mail Stop: BCM225
Houston TX, 77030
Telephone Numbers
- Lab: 713-798-7699
- Fax: 713-798-7610
- Web site Updates/Suggestions: mcfweb@bcm.edu
- Questions/General Inquiry: microarray@bcm.edu
Pricing
Pricing for services in the GPSR can be found on the microarray website.
Services at Texas Children’s Hospital
Experimental Design Consultation
All users of the DLDCC GPSR are required to meet with either the director or co-director to discuss their proposed research. These meeting are generally for one hour and include explanations of the different array technology options available to the user and strategies on how the different array applications will benefit the user’s research. At this time, pricing is also discussed with the user and experiments are designed that maximizes the numbers of samples to achieve the most power while keeping the experiment affordable to each user.
Sample Quality Assurance/Quality Control
Sample quality is one of the most important factors for producing good data. All users intending to utilize one of the genomic profiling services offered in the GPSR must submit the samples to the facility prior to requesting other services. This service is also open to users who just want to gauge the quality of their sample without using our other services. Samples are submitted to the facility through our web-based LIMS and tested for integrity, concentration, and purity. RNA and cDNA samples are analyzed on the Agilent 2100 Bioanalyzer (Agilent Technologies) that utilizes Lab-on-a-Chip technology (Caliper Life Sciences) and the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). Genomic DNA samples are tested using the NanoDrop ND-1000 spectrophotometer and integrity is assessed using agarose gel electrophoresis.
Gene Expression Profiling
Illumina Bead-Array Gene Expression platform
The GPSR offers gene expression profiling utilizing their Illumina BeadChip 500 GX instrument. This instrument platform and the arrays can assay genome wide mRNA expression levels, DASL gene expression (cDNA-mediated annealing, selection, extension, and ligation assay from degraded RNAs such as those derived from formalin-fixed, paraffin-embedded (FFPE) tissues), and microRNA levels as well.
Quantitative Real-Time PCR Gene Expression platform
Users can access Real Time Quantitative PCR (QCPR) services at the GPSR. QPCR allows users to validate gene expression data obtained with arrays as well as to confirm copy number changes identified in their samples. Specific primers and Taqman probes will be designed using PrimerExpress software from Applied Biosystems Inc (ABI). The specificity and uniqueness of the primers will be further checked using in-silico PCR software. The oligos will be synthesized either by ABI or the molecular biology core laboratory in BCM. RNA samples will be reversed transcribed to cDNA using reverse transcription kit from ABI. The primers, probes, DNA or cDNA samples will be put into either the ABI 7000 Prism real time PCR machine or BioRad Icycler real time PCR machine for generation of Ct values. Samples are duplicated in adjacent wells and average Ct will be scored upon completion of the reactions.
Genomic DNA-Based Profiling
SNP Genotyping Platform and Methylation Profiling
DLDCC members can do human SNP genotyping (Affymetrix or Illumina) through the GPSR. Illumina assays for SNP genotyping include the Infinium assay and GoldenGate assay. The platform allows for whole genome SNP analysis, focused and custom SNP genotyping, linkage analysis, and methylation profiling.
Data Analysis
The GPSR works in conjunction with the DLDCC Biostatistics Shared Resource. Users who intend to request data analysis (for SNP genotyping and mRNA expression) help are directed to the Biostatistics Resource for discussions that includes experimental design/consultation. Other analyses are available through the GPSR and they include aCGH analysis, miRNA expression analysis, and Illumina bead-array analysis. The GPSR also collaborates closely the with Bioinformatics Research Center here at BCM for aid in pathway analysis and other database-related issues.
Contact Information
Eastwood Leung, Ph.D.
Assistant Professor
Dan L. Duncan Cancer Center
Dept. of Pediatrics and Dept. of Cellular and Molecular Biology
Phone: 832-824-4373
Email: exleung@texaschildrenshospital.org
Staff
Director: Eastwood Leung, exleung@texaschildrenshospital.org Laboratory Manager: Matthew Folsom, mrfolsom@texaschildrenshospital.org Bioinformatics Programmer: Sergey Torsky, Ph.D., Staff Technician: Sivashankarappa GurusiddappaLocation
Feigin Center
1102 Bates Street, Room C1070.01
Houston TX, 77030
Telephone Numbers
- Lab: 832-824-4354
- Fax: 832-825-4038